As you can see, he's confirmed dead at the end of Persona 3 Game The Journey and Persona 3 the Movie: Winter of Rebirth (#4). However in this headcanon, I used that his body is not cremated and instead was being treated as alive, falling into his deep sleep (in coma condition) right after the ending of the story.
He soon was awoken two years after Persona 4 Arena Ultimax story(2012). He was able to be alive again because he was somehow saved by Elizabeth. Elizabeth used the power she has to separate the life of Makoto Yuki by half. Half of Makoto's life is used at the great seal and the other half is being transfered to Makoto's real body. Due to this event, Makoto couldn't be called that he's totally alive, he's half-dead/half-alive. Aside of being half-alive, he's also ageless means whenever he's having a birthday, he'll always be 21 years old. By the time he was resurrected/awaken, his body was in Tatsumi Memorial Hospital, under the care of Kirijo Group in the hand of his old comrade, Mitsuru Kirijo.
Apparently, him being half-alive gives him several disadvantages. First, he didn't have physical condition as good as he used to be. Second, due to his 'bad' physical condition, he tried to maintain his stamina as long as he could especially about summoning his persona. The power of the wild card has not gone yet, but since changing many personas will only make his power drains faster, he mainly uses 3 Personas; Thanatos, Messiah, and Orpheus Telos.
Since he wanted to repay Elizabeth's deed, he watched over the world, trying to keep away mankind's wishes of calling forth Erebus as the payment.
Being not fully guards the seal makes another disadvantage for Makoto. Sometimes, the Dark Hour will come unexpectedly in random times because of the leaking from the seal. Although the tartarus is no longer there, the shadows will sometimes be seen roaming on the road and needs to be exterminated. The signal of the coming of the Dark Hour will be shown by Makoto himself such as, uncontrollable heartbeat and anything that will make Makoto's body weakened.
He soon was awoken two years after Persona 4 Arena Ultimax story(2012). He was able to be alive again because he was somehow saved by Elizabeth. Elizabeth used the power she has to separate the life of Makoto Yuki by half. Half of Makoto's life is used at the great seal and the other half is being transfered to Makoto's real body. Due to this event, Makoto couldn't be called that he's totally alive, he's half-dead/half-alive. Aside of being half-alive, he's also ageless means whenever he's having a birthday, he'll always be 21 years old. By the time he was resurrected/awaken, his body was in Tatsumi Memorial Hospital, under the care of Kirijo Group in the hand of his old comrade, Mitsuru Kirijo.
Apparently, him being half-alive gives him several disadvantages. First, he didn't have physical condition as good as he used to be. Second, due to his 'bad' physical condition, he tried to maintain his stamina as long as he could especially about summoning his persona. The power of the wild card has not gone yet, but since changing many personas will only make his power drains faster, he mainly uses 3 Personas; Thanatos, Messiah, and Orpheus Telos.
Since he wanted to repay Elizabeth's deed, he watched over the world, trying to keep away mankind's wishes of calling forth Erebus as the payment.
Being not fully guards the seal makes another disadvantage for Makoto. Sometimes, the Dark Hour will come unexpectedly in random times because of the leaking from the seal. Although the tartarus is no longer there, the shadows will sometimes be seen roaming on the road and needs to be exterminated. The signal of the coming of the Dark Hour will be shown by Makoto himself such as, uncontrollable heartbeat and anything that will make Makoto's body weakened.